I suspect your bone/joint pains are from the osteopenia. You've heard of "growing pains"? Whether you're losing bone or gaining bone, (which may be what's happening now that your D level is back to normal) you're going to have aches and pains, especially in the long bones of your arms and legs.

Since you have celiac you might want to watch for symptoms of autoimmune thyroid disease, since both hypothyroid and hyperthyroid are very common in celiacs. Hyperthyroid can sometimes "steal" calcium away from the bones, so if you don't improve in the coming months, it's something to consider.